G C A T T A C G G C A T genes Article Autosomal Dominantly Inherited GREB1L Variants in Individuals with Profound Sensorineural Hearing Impairment Isabelle Schrauwen 1,* , Khurram Liaqat 2, Isabelle Schatteman 3 , Thashi Bharadwaj 1, Abdul Nasir 4 , Anushree Acharya 1, Wasim Ahmad 5, Guy Van Camp 6 and Suzanne M. Leal 1 1 Center for Statistical Genetics, Sergievsky Center, Taub Institute for Alzheimer’s Disease and the Aging Brain, and the Department of Neurology, Columbia University Medical Center, New York, NY 10032, USA; [email protected] (T.B.); [email protected] (A.A.); [email protected] (S.M.L.) 2 Department of Biotechnology, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan; [email protected] 3 Department of ENT, St-Augustinus Hospital Antwerp, 2610 Antwerp, Belgium; [email protected] 4 Synthetic Protein Engineering Lab (SPEL), Department of Molecular Science and Technology, Ajou University, Suwon 443-749, Korea; [email protected] 5 Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan; [email protected] 6 Center of Medical Genetics, University of Antwerp & Antwerp University Hospital, 2650 Antwerp, Belgium; [email protected] * Correspondence: [email protected]; Tel.: +1-(212)-304-5272 Received: 1 June 2020; Accepted: 20 June 2020; Published: 23 June 2020 Abstract: Congenital hearing impairment is a sensory disorder that is genetically highly heterogeneous. By performing exome sequencing in two families with congenital nonsyndromic profound sensorineural hearing loss (SNHL), we identified autosomal dominantly inherited missense variants [p.(Asn283Ser); p.(Thr116Ile)] in GREB1L, a neural crest regulatory molecule. The p.(Thr116Ile) variant was also associated with bilateral cochlear aplasia and cochlear nerve aplasia upon temporal bone imaging, an ultra-rare phenotype previously seen in patients with de novo GREB1L variants. / An important role of GREB1L in normal ear development has also been demonstrated by greb1l− − zebrafish, which show an abnormal sensory epithelia innervation. Last, we performed a review of all disease-associated variation described in GREB1L, as it has also been implicated in renal, bladder and genital malformations. We show that the spectrum of features associated with GREB1L is broad, variable and with a high level of reduced penetrance, which is typically characteristic of neurocristopathies. So far, seven GREB1L variants (14%) have been associated with ear-related abnormalities. In conclusion, these results show that autosomal dominantly inherited variants in GREB1L cause profound SNHL. Furthermore, we provide an overview of the phenotypic spectrum associated with GREB1L variants and strengthen the evidence of the involvement of GREB1L in human hearing. Keywords: autosomal dominant inheritance; exome sequencing; GREB1L; profound nonsyndromic hearing impairment; cochlear aplasia; cochlear nerve aplasia; neural crest; neurocristopathy 1. Introduction Childhood hearing impairment (HI) is associated with impaired language acquisition, learning, speech development and affects 34 million children worldwide (World Health Organization). Approximately 1/1000 children are born with hearing loss, of which approximately 80% is genetic [1]. Genes 2020, 11, 687; doi:10.3390/genes11060687 www.mdpi.com/journal/genes Genes 2020, 11, 687 2 of 18 HI can be part of a syndrome with the presence of other medical anomalies, or it can be nonsyndromic. Currently, 120 nonsyndromic HI genes have been identified, with 59% having an autosomal recessive (AR), 37% an autosomal dominant (AD), and 5% an X-linked mode of inheritance (Hereditary hearing loss homepage). However, many genes remain to be identified due to the complexity of the hearing system and due to the understudy of some ancestries [2]. Nonsyndromic HI has no association with additional features or abnormalities. However, it can be associated with abnormalities of the middle ear and/or inner ear [1]. A large number of these abnormalities are mild, but bilateral cochlear aplasia, i.e., bilateral absence of the cochlea, is an ultra-rare and severe developmental abnormality of the inner ear. Approximately 0.3% of children with congenital sensorineural HI are estimated to have bilateral cochlear aplasia [3]. However, this estimate is predominately based on children who were candidates for a cochlear implant, and they usually present with severe-to-profound HI [3–5]. We previously identified de novo loss-of-function variants in GREB1L in two individuals with profound nonsyndromic HI with inner ear and cochleovestibular nerve (or 8th cranial) malformations (Table1)[ 5,6]. Affected individuals had either absent cochleae bilaterally [p.(Glu1410fs)] or an absent cochlea on the right and incomplete partition type I on the left [p.(Arg328*)]. Both individuals also / displayed abnormalities of their vestibules and absent 8th cranial nerves [6]. In addition, greb1l− − zebrafish exhibit a loss of and/or abnormal sensory epithelia innervation, including a loss of the anterior cristae nerve and an abnormal innervation pathway from the occipital lateral line neuromast. These findings in humans and model organisms confirm the importance of GREB1L in sensory innervation [6]. Furthermore, Greb1l is widely expressed during craniofacial development, including / the otic vesicle [6,7], and Greb1l− − mice are embryological lethal and demonstrate severe abnormalities, +/ including craniofacial and renal abnormalities [8]. Greb1l − mice show an abnormal embryo size, growth retardation [9] and mild abnormalities to their kidneys and ureters [8]. Genes 2020, 11, 687 3 of 18 Table 1. Variants identified in GREB1L associated with nonsyndromic hearing impairment. Predicted CADD Splicing Family Variant Inheritance cDNA Variant AA Change gnomAD Score GERP++RS Effect Phenotype ACMG 3 Study Type Segregation Model Change 1 Effect (v1.3) Prediction 2 profound bilateral SNHI; UCA (right); Trio de novo AD splicing c.4368G>T p.(Glu1410fs) absent 26 5.17 splice site loss P[6] UIP-I (left); BVES + SCC; BCNA profound bilateral SNHI; Trio de novo AD nonsense c.982C>T p.(Arg328*) absent 38 4.52 NA P[6] BCA; BVES + SCC; BCNA missense/ profound This study Family inherited AD c.848A>G p.(Asn283Ser) absent 10 3.44 ESE site loss LP splicing bilateral SNHI 4 (Family 1) profound bilateral SNHI; This study Trio inherited 5 AD missense c.347C>T p.(Thr116Ile) absent 30 5.25 NA VUS BCA; BVES + (Family 2) SCC; BCNA 1 Based on NM_001142966.2; 2 Based on Human splicing finder (v.3.1), ESEfinder (v2.0) [10,11]. 3 Classified based on the American College of Medical Genetics (ACMG) guidelines: P, Pathogenic; LP, likely pathogenic; VUS, variant of unknown significance [12]. 4 Inner ear not evaluated via imaging. 5 Maternal reduced penetrance; AD, Autosomal Dominant; BCA, bilateral cochlear aplasia; BCNA, bilateral cochlear nerve aplasia; BVES + SCC: bilateral dysplastic vestibule and semicircular canals; ESE, exonic splicing enhancer; NA, Not applicable; SNHI, sensorineural hearing impairment; UCA, unilateral cochlear aplasia; UIP-I, unilateral incomplete partition type I. Genes 2020, 11, 687 4 of 18 In addition, de novo or autosomal dominantly inherited variants (often with reduced penetrance) have previously been implicated in individuals with renal, bladder and genital malformations [8,13,14]. Renal hypoplasia/aplasia 3 (RHDA3) is a severe developmental disorder characterized by abnormal kidney development and is caused by heterozygous GREB1L variants. Although the phenotype can be highly variable, the disorder falls within the most severe end of the spectrum of congenital anomalies of the kidney and urinary tract. In many of these cases, children were aborted or stillborn due to the severity of the malformations, such as bilateral renal aplasia [8,13,14]. In this article, we have, for the first time, identified a family with congenital profound HI that segregates a missense variant in GREB1L with an AD mode of inheritance and also report on an additional case with bilateral cochlear and cochlear nerve aplasia with a GREB1L variant. 2. Materials and Methods 2.1. Patient Recruitment and Clinical Assessment The study was approved by the ethics committee of the Quaid-i-Azam University (IRB-QAU-153), University of Antwerp (B3002020000073) and the Institutional review board of Columbia University (IRB-AAAS2343). Informed consent and peripheral blood samples were obtained from all individuals of a non-consanguineous Pakistani family with deafness (Family 1 [4697]; Figure1A) and a non-consanguineous Egyptian family with deafness (Family 2 [BAIE1]; Figure1B). DNA was extracted using a phenol-chloroform procedure for the Pakistani family [15] and using magnetic beads with the chemagic™ blood DNA kit on a chemagic™ Prime™ instrument (PerkinElmer, Waltham, MA, USA) for the Egyptian family. The patient evaluation included a clinical history, physical, audiological and vestibular examination. Computed tomography (CT) and magnetic resonance imaging (MRI) of the temporal bone were performed in the Egyptian patient to identify the presence of cochleovestibular malformations (Family 2). Unfortunately, we were unable to perform CT or MRI on the Pakistani family (Family 1) due to the remote location of these individuals in the Khyber Pakhtunkhwa province, Pakistan. GenesGenes 20202020,, 1111,, x 687 FOR PEER REVIEW 55 of of 16 18 Figure 1. Segregation of the GREB1L missense variants in both families, audiological